On the molecular evolution of the Plasmodium falciparum

Abstract:

Research in the Plasmodium falciparum molecular evolution field has
predominantly comprised three distinct areas: phylogenetics, host-parasite coevolution
and evolutionary genomics. These areas have greatly enhanced our
understanding of the early origins of the phylum Apicomplexa, the emergence of
P. falciparum, and the co-evolution between parasite and human hereditary
erythrocyte disorders. In addition, the genome sequencing projects have
elucidated the complexity and extremely unusual nature of the parasite genome.
Some aspects of parasite molecular evolution, however, are controversial, such as
human pyruvate kinase (PK) deficiency and P. falciparum virulence coevolution.
Other aspects, like Plasmodium whole genome evolution have
remained unexplored.
This thesis includes a collection of manuscripts that address aspects of the broad
field of P. falciparum molecular evolution. The first deals with the limitations of
bioinformatic methods as applied to P. falciparum, which have arisen due to the
unusual nature of the parasite genome, such as the extreme nucleotide bias.
Although conventional bioinformatics can partially accommodate and
compensate for the genome idiosyncrasies, these limitations have hampered
progress significantly. A novel alignment method, termed FIRE (Functional
Inference using the Rates of Evolution) was therefore developed. FIRE uses the
evolutionary constraints at codon sites to align sequences and infer domain
function and overcomes the problem of poor sequence similarity, which is
commonly encountered between P. falciparum and other taxa. A second aspect
addressed in this thesis, is the host-parasite relationship in the context of PK
deficiency. It was demonstrated that PK deficient erythrocytes are dramatically
resistant to parasite infection, providing in vitro evidence for this phenomenon
and confirming this aspect of host-parasite co-evolution.
The unexplored field of parasite genome evolution was initiated in this thesis by
investigating two major role-players in genome dynamics, mobile genetic elements (MGEs) and programmed cell death (PCD). MGEs were absent in P.
falciparum, possibly due to a geno-protective mechanism, which increased the
AT nucleotide bias. Interestingly, the parasite telomerase reverse transcriptase,
which is a domesticated MGE, was identified. In addition, there is genomic
evidence for the second determinant, a classical PCD pathway. Intriguingly,
functional and structural evidence for a p53-like DNA-binding domain, which
plays a key role in genome evolution, was obtained. Using MGEs and PCD as
examples, a theoretical framework for investigating genome dynamics was
developed. The framework proposes an ecological approach to genome evolution,
in which a trade-off exists between two opposing processes: the generation of
diversity by factors such as MGEs and the maintenance of integrity by factors
like PCD. The framework is suggested for proposing and testing hypotheses to
investigate the origins and evolution of the P. falciparum genome.
Finally, a novel approach, termed Evolutionary Patterning (EP), was developed to
limit the problem of parasite drug resistance and demonstrates the value of
employing molecular evolution to address biomedical challenges.
Some of this work, such as the FIRE method, the host-parasite co-evolution
studies, the PCD findings and the EP approach have been incorporated in grant
proposals and adopted in future projects. It is hoped that this research will be
used to further our understanding of P. falciparum evolution and advance the
efforts to control this deadly pathogen.